Phytochrome-interacting factors have both shared and distinct biological roles
- 1k Downloads
Phytochromes are plant photoreceptors that perceive red and far-red light. Upon the perception of light in Arabidopsis, light-activated phytochromes enter the nucleus and act on a set of interacting proteins, modulating their activities and thereby altering the expression levels of ∼10% of the organism’s entire gene complement. Phytochromeinteracting factors (PIFs) belonging to Arabidopsis basic helix-loop-helix (bHLH) subgroup 15 are key interacting proteins that play negative roles in light responses. Their activities are post-translationally countered by light-activated phytochromes, which promote the degradation of PIFs and directly or indirectly inhibit their binding to DNA. The PIFs share a high degree of similarity, but examinations of pif single and multiple mutants have indicated that they have shared and distinct functions in various developmental and physiological processes. These are believed to stem from differences in both intrinsic protein properties and their gene expression patterns. In an effort to clarify the basis of these shared and distinct functions, we compared recently published genome-wide ChIP data, developmental gene expression maps, and responses to various stimuli for the various PIFs. Based on our observations, we propose that the biological roles of PIFs stem from their shared and distinct DNA binding targets and specific gene expression patterns.
KeywordsbHLH transcription factor gene expression analysis light signaling phytochrome phytochrome-interacting factor
Unable to display preview. Download preview PDF.
- Casal, J.J. (2013). Photoreceptor signaling networks in plant responses to shade. Ann. Rev. Plant Biol. [Epub ahead of print]Google Scholar
- Filichkin, S.A., Breton, G., Priest, H.D., Dharmawardhana, P., Jaiswal, P., Fox, S.E., Michael, T.P., Chory, J., Kay, S.A., and Mockler, T.C. (2011). Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cisregulatory modules. PLoS One 6, e16907.PubMedCrossRefGoogle Scholar
- Hornitschek, P., Kohnen, M.V., Lorrain, S., Rougemont, J., Ljung, K., Lopez-Vidriero, I., Franco-Zorrilla, J.M., Solano, R., Trevisan, M., Pradervand, S., et al. (2012). Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling. Plant J. 71, 699–711.PubMedCrossRefGoogle Scholar
- Kidokoro, S., Maruyama, K., Nakashima, K., Imura, Y., Narusaka, Y., Shinwari, Z.K., Osakabe, Y., Fujita, Y., Mizoi, J., Shinozaki, K., et al. (2009). The phytochrome-interacting factor PIF7 negatively regulates DREB1 expression under circadian control in Arabidopsis. Plant Physiol. 151, 2046–2057.PubMedCrossRefGoogle Scholar
- Laubinger, S., Zeller, G., Henz, S.R., Sachsenberg, T., Widmer, C.K., Naouar, N., Vuylsteke, M., Scholkopf, B., Ratsch, G., and Weigel, D. (2008). At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol. 9, R112.PubMedCrossRefGoogle Scholar
- Leivar, P., Monte, E., Al-Sady, B., Carle, C., Storer, A., Alonso, J.M., Ecker, J.R., and Quail, P.H. (2008b). The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. Plant Cell 20, 337–352.PubMedCrossRefGoogle Scholar
- Leivar, P., Tepperman, J.M., Monte, E., Calderon, R.H., Liu, T.L., and Quail, P.H. (2009). Definition of early transcriptional circuitry involved in light-induced reversal of PIF-imposed repression of photomorphogenesis in young Arabidopsis seedlings. Plant Cell 21, 3535–3553.PubMedCrossRefGoogle Scholar
- Leivar, P., Tepperman, J.M., Cohn, M.M., Monte, E., Al-Sady, B., Erickson, E., and Quail, P.H. (2012). Dynamic antagonism between phytochromes and PIF family basic helix-loop-helix factors induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis. Plant Cell 24, 1398–1419.PubMedCrossRefGoogle Scholar
- Mockler, T.C., Michael, T.P., Priest, H.D., Shen, R., Sullivan, C.M., Givan, S.A., McEntee, C., Kay, S.A., and Chory, J. (2007). The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harb. Symp. Quant. Biol. 72, 353–363.PubMedCrossRefGoogle Scholar
- Todaka, D., Nakashima, K., Maruyama, K., Kidokoro, S., Osakabe, Y., Ito, Y., Matsukura, S., Fujita, Y., Yoshiwara, K., Ohme-Takagi, M., et al. (2012). Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress. Proc. Natl. Acad. Sci. USA 109, 15947–15952.PubMedCrossRefGoogle Scholar
- Zhang, Y., Mayba, O., Pfeiffer, A., Shi, H., Tepperman, J.M., Speed, T.P., and Quail, P.H. (2013). A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis. PLoS Genet. 9, e1003244.PubMedCrossRefGoogle Scholar